National Center for Design of
Biomimetic Nanoconductors

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Steve Plimpton

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Steve Plimpton is a distinguished member of the technical staff in the Computational Biology group at Sandia National Laboratory. He is involved in a dozen or more projects to develop parallel algorithms and simulation codes in various scientific disciplines: cell modeling, atomistic modeling of biomolecules, gene linkage analysis, quantum density functional theory, radiation transport, electromagnetics, microscopy image formation, radar image analysis, plasma physics, grain growth, low-density fluid flow, etc. He is also the chief developer of open-source parallel LAMMPS molecular dynamics code, www.cs.sandia.gov/~sjplimp/lammps.html.

Research

Plimpton’s role in the Center is to develop an integrated modeling platform for three-dimensional reaction-diffusion processes. His preliminary continuum cell modeling work has been done primarily with a Sandia high-performance computing tool called MPSalsa, which is an unstructured finite element (FE) code for solving chemically reacting flow problems on massively parallel computers.

Plimpton has also developed an initial version of a particle-based spatial cell modeling code called ChemCell (Plimpton, 2003). The cellular geometry is represented by triangulated membrane surface grids which can be simple smooth surfaces or image reconstructions of actual cells. Particles representing proteins or other biomolecules diffuse via Brownian motion both volumetrically (3-D) or on surfaces (2-D). Reactions between nearby particles occur via Monte Carlo rules and can represent dimerization, ligand binding or unbinding, complex formation, transporter formation or activation, etc. In principle, protein networks of any kind (metabolic, signaling, regulatory) can be encoded in a ChemCell model, provided inputs are known.

This integrated 3-dimensional stochastic/continuum modeling framework will become integral to biobattery and other device design utilizing conductors in nanopore arrays.

Related Publications

S. J. Plimpton and A. Slepoy, "ChemCell: A Particle-Based Model of Protein Chemistry and Diffusion in Microbial Cells", Sandia National Laboratories Technical Report 2003-4509 (2003).

S. J. Plimpton, B. Hendrickson, S. Burns, W. Mclendon III, L Rauchwerger, "Parallel Algorithms for Sn Transport on Unstructured Grids", to appear in Nuclear Science and Engineering (2005).

S. J. Plimpton, D. B. Seidel, M. F. Pasik, R. S. Coats, G. R. Montry, "A Load-Balancing Algorithm for a Parallel Electromagnetic Particle-in-Cell Code", Comp Phys Comm, 152, 227-241 (2003).

G. C. Conant, S. J. Plimpton, W. Old, A. Wagner, P. R. Fain, T. R. Pacheco, and G. Heffelfinger, "Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures", J Parallel and Distributed Computing, 63, 674-682 (2003).

S. J. Plimpton, B. Hendrickson, J. Stewart, R. Cochran, "A Parallel Rendezvous Algorithm for Interpolation Between Multiple Grids", J Parallel and Distributed Computing, 64, 266-276 (2004).

L. E. Silbert, G. S. Grest, S. J. Plimpton, D. Levine, "Boundary Effects and Self-organization in Dense Granular Flows", Physics of Fluids, 14, 2637-2646 (2002).

C. L. Kelchner, S. J. Plimpton, J. C. Hamilton, "Dislocation Nucleation and Defect Structure During Surface Indentation", Phys Rev B, 58, 11085-11088 (1998).

S. J. Plimpton, S. Attaway, B. Hendrickson, J. Swegle, C. Vaughan, D. Gardner, "Parallel Transient Dynamics Simulations: Algorithms for Contact Detection and Smoothed Particle Hydrodynamics", J Parallel Dist Comp, 50, 104-122 (1998).

C. Donati, J. F. Douglas, W. Kob, S. J. Plimpton, P. H. Poole, S. C. Glotzer, "Stringlike Cooperative Motion in a Supercooled Liquid", Phys Rev Lett, 80, 2338-2341 (1998).

M. J. Stevens and S. J. Plimpton, "The Effect of Added Salt on Polyelectrolyte Structure", Eur Phys J B, 2, 341-345 (1998).

S. J. Plimpton and B. A. Hendrickson, "A New Parallel Method for Molecular-Dynamics Simulation of Macromolecular Systems", J Comp Chem, 17, 326-337 (1996).

S. J. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics", J Comp Phys, 117, 1-19 (1995). (cited 150 times)

Related Links

Comprehensive List of Publications

Steve Plimpton at Sandia National Labs

Sandia National Laboratories

The National Center for Design of Biomimetic Nanoconductors is funded by Grant Number PHS 2 PN2 EY016570B from the National Institutes of Health through the NIH Roadmap for Medical Research and is based at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. Partner institutions include Yale University, University of Southern California, University of Chicago, Illinois Institute of Technology, Sandia National Laboratories, Argonne National Laboratory, Oxford University, Wabash College, University of California, Davis, nanoHUB at Purdue University, and the University of New Mexico.